Reactions Rules Kinetics Pane

The reaction properties panel is used to display and edit kinetics and annotations for a reaction rule.

The kinetics pane shows the Reaction Name and a table of the kinetic terms used to define the reaction rate. Items in brown cannot be edited.

Note that the rate defined for a reaction rule may differ from the actual reaction rate. Reaction rules can currently only be defined using mass action kinetics.

• For a reaction generated by a rule, the rate law is defined as the microscopic forward rate times the concentration(s) of the reactant species minus the microscopic reverse rate times the concentration(s) of the product species.
• The microscopic rate is a rate derived from first principles based on the probability that particles in an ideal gas will collide. However, a reaction rule can generate multiple reactions and in some reactions the total number of product particles will be the same as the reactant particles; in this case the rate is automatically adjusted by BioNetGen network generation engine. For example, if the rule rate for a+b -> is k, and the rule generates a reaction c+c-> c2, then the rate for the reaction will be 0.5k
• Forward rate and reverse rate may be any expressions, but cannot depend on concentrations of other species.

Edit the reaction name using the text field. A name already given to another reaction will be rejected.

Make reaction reversible by checking the Reversible box. This box must be checked to enable specification of the reverse rate. When the box is checked, the user can edit the reverse rate expression. Checking the Reversible box in the kinetic pane also checks the box in the editor pane, and vice versa.

Edit the expression for the forward rate and, if the reversible box is checked, for the reverse rate in the Expression column. If references to new parameters are added, new rows will automatically be added for those parameters. An expression for each new parameter must be added in the Expression column. Parameters can be set to global or local using the checkbox. The reaction rule rate is always local; species concentrations and universal constants are always global.

Edit units for the rate expression in the Units column. Incompatible units will be silently rejected.

Add annotations in the Annotation text field, which can be shown or hidden by selecting the plus or minus sign next to the Annotations text.